Image Processing in Cryo-Electron Microscopy of Single
Particles: The Power of Combining Methods

C 2021

Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods

S. SORZANO, Carlos Oscar, Amaya JIMÉNEZ-MORENO, David MALUENDA, Erney RAMÍREZ-APORTELA, Marta MARTÍNEZ et. al.

Basic information

Original name

Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods

Authors

S. SORZANO, Carlos Oscar, Amaya JIMÉNEZ-MORENO, David MALUENDA, Erney RAMÍREZ-APORTELA, Marta MARTÍNEZ, Ana CUERVO, Roberto MELERO, Jose Javier CONESA, Ruben SÁNCHEZ-GARCÍA, David STŘELÁK (203 Czech Republic, belonging to the institution), Jiří FILIPOVIČ (203 Czech Republic, guarantor, belonging to the institution), Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, David HERREROS, Pablo CONESA, Laura DEL CAÑO, Yunior FONSECA, Jorge JIMÉNEZ DE LA MORENA, Jose Ramon MACÍAS, Patricia LOSANA, Roberto MARABINI and Jose-Maria CARAZO

Edition

Clifton, N.J. Structural Proteomics, p. 257-289, 33 pp. Methods in Molecular Biology, 2021

Publisher

Springer US

Other information

Language

English

Type of outcome

Kapitola resp. kapitoly v odborné knize

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

RIV identification code

RIV/00216224:14330/21:00122290

Organization unit

Faculty of Informatics

ISBN

978-1-0716-1405-1

DOI

http://dx.doi.org/10.1007/978-1-0716-1406-8_13

UT WoS

000691017300014

Keywords in English

Cryo-electron microscopy; Image processing; Scipion; Single particle

Abstract

V originále

Cryo-electron microscopy has established as a mature structural biology technique to elucidate the three-dimensional structure of biological macromolecules. The Coulomb potential of the sample is imaged by an electron beam, and fast semi-conductor detectors produce movies of the sample under study. These movies have to be further processed by a whole pipeline of image-processing algorithms that produce the final structure of the macromolecule. In this chapter, we illustrate this whole processing pipeline putting in value the strength of "meta algorithms," which are the combination of several algorithms, each one with different mathematical rationale, in order to distinguish correctly from incorrectly estimated parameters. We show how this strategy leads to superior performance of the whole pipeline as well as more confident assessments about the reconstructed structures. The "meta algorithms" strategy is common to many fields and, in particular, it has provided excellent results in bioinformatics. We illustrate this combination using the workflow engine, Scipion.

Links

EF16_013/0001802, research and development project

Name: CERIT Scientific Cloud

MUNI/A/1411/2019, interní kód MU

Name: Aplikovaný výzkum: softwarové architektury kritických infrastruktur, bezpečnost počítačových systémů, zpracování přirozeného jazyka a jazykové inženýrství, vizualizaci velkých dat a rozšířená realita.

Investor: Masaryk University, Category A

Citovat

S. SORZANO, Carlos Oscar, Amaya JIMÉNEZ-MORENO, David MALUENDA, Erney RAMÍREZ-APORTELA, Marta MARTÍNEZ, Ana CUERVO, Roberto MELERO, Jose Javier CONESA, Ruben SÁNCHEZ-GARCÍA, David STŘELÁK, Jiří FILIPOVIČ, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, David HERREROS, Pablo CONESA, Laura DEL CAÑO, Yunior FONSECA, Jorge JIMÉNEZ DE LA MORENA, Jose Ramon MACÍAS, Patricia LOSANA, Roberto MARABINI and Jose-Maria CARAZO. Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods. In Structural Proteomics. Clifton, N.J.: Springer US, 2021, p. 257-289. Methods in Molecular Biology. ISBN 978-1-0716-1405-1. Available from: https://dx.doi.org/10.1007/978-1-0716-1406-8_13.

@inbook{1790524,
   author = {S. Sorzano, Carlos Oscar and JiménezandMoreno, Amaya and Maluenda, David and RamírezandAportela, Erney and Martínez, Marta and Cuervo, Ana and Melero, Roberto and Conesa, Jose Javier and SánchezandGarcía, Ruben and Střelák, David and Filipovič, Jiří and FernándezandGiménez, Estrella and de IsidroandGómez, Federico and Herreros, David and Conesa, Pablo and del Caño, Laura and Fonseca, Yunior and Jiménez de la Morena, Jorge and Macías, Jose Ramon and Losana, Patricia and Marabini, Roberto and Carazo, JoseandMaria},
   address = {Clifton, N.J.},
   booktitle = {Structural Proteomics},
   doi = {http://dx.doi.org/10.1007/978-1-0716-1406-8_13},
   keywords = {Cryo-electron microscopy; Image processing; Scipion; Single particle},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Clifton, N.J.},
   isbn = {978-1-0716-1405-1},
   pages = {257-289},
   publisher = {Springer US},
   title = {Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods},
   year = {2021}
}

TY  - CHAP
ID  - 1790524
AU  - S. Sorzano, Carlos Oscar - Jiménez-Moreno, Amaya - Maluenda, David - Ramírez-Aportela, Erney - Martínez, Marta - Cuervo, Ana - Melero, Roberto - Conesa, Jose Javier - Sánchez-García, Ruben - Střelák, David - Filipovič, Jiří - Fernández-Giménez, Estrella - de Isidro-Gómez, Federico - Herreros, David - Conesa, Pablo - del Caño, Laura - Fonseca, Yunior - Jiménez de la Morena, Jorge - Macías, Jose Ramon - Losana, Patricia - Marabini, Roberto - Carazo, Jose-Maria
PY  - 2021
TI  - Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods
VL  - Methods in Molecular Biology
PB  - Springer US
CY  - Clifton, N.J.
SN  - 9781071614051
KW  - Cryo-electron microscopy
KW  - Image processing
KW  - Scipion
KW  - Single particle
N2  - Cryo-electron microscopy has established as a mature structural biology technique to elucidate the three-dimensional structure of biological macromolecules. The Coulomb potential of the sample is imaged by an electron beam, and fast semi-conductor detectors produce movies of the sample under study. These movies have to be further processed by a whole pipeline of image-processing algorithms that produce the final structure of the macromolecule. In this chapter, we illustrate this whole processing pipeline putting in value the strength of "meta algorithms," which are the combination of several algorithms, each one with different mathematical rationale, in order to distinguish correctly from incorrectly estimated parameters. We show how this strategy leads to superior performance of the whole pipeline as well as more confident assessments about the reconstructed structures. The "meta algorithms" strategy is common to many fields and, in particular, it has provided excellent results in bioinformatics. We illustrate this combination using the workflow engine, Scipion.
ER  -

S. SORZANO, Carlos Oscar, Amaya JIMÉNEZ-MORENO, David MALUENDA, Erney RAMÍREZ-APORTELA, Marta MARTÍNEZ, Ana CUERVO, Roberto MELERO, Jose Javier CONESA, Ruben SÁNCHEZ-GARCÍA, David STŘELÁK, Jiří FILIPOVIČ, Estrella FERNÁNDEZ-GIMÉNEZ, Federico DE ISIDRO-GÓMEZ, David HERREROS, Pablo CONESA, Laura DEL CAÑO, Yunior FONSECA, Jorge JIMÉNEZ DE LA MORENA, Jose Ramon MACÍAS, Patricia LOSANA, Roberto MARABINI and Jose-Maria CARAZO. Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods. In \textit{Structural Proteomics}. Clifton, N.J.: Springer US, 2021, p.~257-289. Methods in Molecular Biology. ISBN~978-1-0716-1405-1. Available from: https://dx.doi.org/10.1007/978-1-0716-1406-8\_{}13.

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